protected override GraphData CreateGraphData(SrmDocument document, PeptideGroupDocNode selectedProtein, TransitionGroupDocNode selectedGroup, DisplayTypeChrom displayType)
{
int? result = null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.single)
result = GraphSummary.ResultsIndex;
return new AreaGraphData(document, selectedGroup, selectedProtein, result, displayType, PaneKey);
}
private List <PointPairList> GetPointPairLists(TransitionGroupDocNode nodeGroup,
DisplayTypeChrom displayType)
{
var transitionGroupChromInfoDatas = TransitionGroupChromInfoData.GetTransitionGroupChromInfoDatas(
_document.Settings.MeasuredResults, nodeGroup.Results);
return(MakePointPairLists(displayType, transitionGroupChromInfoDatas, IsMissingValue, CreatePointPair));
}
public MassErrorGraphData(SrmDocument document,
IdentityPath identityPath,
DisplayTypeChrom displayType,
ReplicateGroupOp replicateGroupOp,
PaneKey paneKey)
: base(document, identityPath, displayType, replicateGroupOp, paneKey)
{
}
protected override GraphData CreateGraphData(SrmDocument document, PeptideGroupDocNode selectedProtein, TransitionGroupDocNode selectedGroup, DisplayTypeChrom displayType)
{
int? result = null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.single)
result = GraphSummary.ResultsIndex;
return new RTGraphData(document, selectedGroup, selectedProtein, result, displayType, GraphSummary.StateProvider.GetRetentionTimeTransformOperation());
}
protected GraphData(SrmDocument document, DocNode docNode, DisplayTypeChrom displayType, GraphValues.ReplicateGroupOp replicateGroupOp, PaneKey paneKey)
{
_document = document;
_docNode = docNode;
_displayType = displayType;
ReplicateGroupOp = replicateGroupOp;
_paneKey = paneKey;
}
protected GraphData(SrmDocument document, IEnumerable <IdentityPath> selectedDocNodePaths, DisplayTypeChrom displayType,
ReplicateGroupOp replicateGroupOp, PaneKey paneKey)
{
_document = document;
_selectedDocNodePaths = ImmutableList.ValueOf(selectedDocNodePaths);
_displayType = displayType;
ReplicateGroupOp = replicateGroupOp;
_paneKey = paneKey;
}
public AreaGraphData(SrmDocument document,
TransitionGroupDocNode selectedGroup,
PeptideGroupDocNode selectedProtein,
int? result,
DisplayTypeChrom displayType,
PaneKey paneKey)
: base(document, selectedGroup, selectedProtein, result, displayType, null, paneKey)
{
}
public AreaGraphData(SrmDocument document,
TransitionGroupDocNode selectedGroup,
PeptideGroupDocNode selectedProtein,
int?result,
DisplayTypeChrom displayType,
PaneKey paneKey)
: base(document, selectedGroup, selectedProtein, result, displayType, null, paneKey)
{
}
public RTGraphData(SrmDocument document,
TransitionGroupDocNode selectedGroup,
PeptideGroupDocNode selectedProtein,
int?result,
DisplayTypeChrom displayType,
GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp
)
: base(document, selectedGroup, selectedProtein, result, displayType, retentionTimeTransformOp, PaneKey.DEFAULT)
{
}
private List <PointPairList> GetPointPairLists(TransitionGroupDocNode nodeGroup,
TransitionDocNode nodeTran,
DisplayTypeChrom displayType)
{
if (!IncludeTransition(nodeTran))
{
return(new List <PointPairList>());
}
var transitionChromInfoDatas = TransitionChromInfoData.GetTransitionChromInfoDatas(
_document.Settings.MeasuredResults, nodeTran.Results);
return(MakePointPairLists(displayType, transitionChromInfoDatas, IsMissingValue, CreatePointPair));
}
public AreaGraphData(SrmDocument document,
DocNode docNode,
DisplayTypeChrom displayType,
GraphValues.ReplicateGroupOp replicateGroupOp,
int ratioIndex,
AreaNormalizeToData normalize,
AreaExpectedValue expectedVisible,
PaneKey paneKey)
: base(document, docNode, displayType, replicateGroupOp, paneKey)
{
_docNode = docNode;
_ratioIndex = ratioIndex;
_normalize = normalize;
_expectedVisible = expectedVisible;
}
protected abstract GraphData CreateGraphData(SrmDocument document, PeptideGroupDocNode selectedProtein,
TransitionGroupDocNode selectedGroup, DisplayTypeChrom displayType);
public AreaGraphData(SrmDocument document,
DocNode docNode,
DisplayTypeChrom displayType,
GraphValues.ReplicateGroupOp replicateGroupOp,
int ratioIndex,
AreaNormalizeToData normalize,
AreaExpectedValue expectedVisible,
PaneKey paneKey)
: base(document, docNode, displayType, replicateGroupOp, paneKey)
{
_docNode = docNode;
_ratioIndex = ratioIndex;
_normalize = normalize;
_expectedVisible = expectedVisible;
}
protected GraphData(SrmDocument document, TransitionGroupDocNode selectedGroup, PeptideGroupDocNode selectedProtein,
int? iResult, DisplayTypeChrom displayType, GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp,
PaneKey paneKey)
{
RetentionTimeTransformOp = retentionTimeTransformOp;
// Determine the shortest possible unique ID for each peptide or molecule
var sequences = new List<Tuple<string, bool>>();
foreach (var nodePep in document.Molecules)
sequences.Add(new Tuple<string, bool>(nodePep.RawTextId, nodePep.IsProteomic));
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
int pointListCount = 0;
var dictTypeToSet = new Dictionary<IsotopeLabelType, int>();
bool onePointPerPeptide = PeptideOrder == SummaryPeptideOrder.document &&
null != paneKey.IsotopeLabelType;
// Figure out how many point lists to create
bool displayTotals = (displayType == DisplayTypeChrom.total);
if (displayTotals)
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
if (!dictTypeToSet.ContainsKey(labelType))
dictTypeToSet.Add(labelType, pointListCount++);
}
}
else
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointListCount = Math.Max(pointListCount, GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).Count());
}
}
// Build the list of points to show.
var listPoints = new List<GraphPointData>();
foreach (PeptideGroupDocNode nodeGroupPep in document.MoleculeGroups)
{
if (AreaGraphController.AreaScope == AreaScope.protein)
{
if (!ReferenceEquals(nodeGroupPep, selectedProtein))
continue;
}
foreach (PeptideDocNode nodePep in nodeGroupPep.Children)
{
bool addBlankPoint = onePointPerPeptide &&
!nodePep.TransitionGroups.Any(paneKey.IncludesTransitionGroup);
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var path = new IdentityPath(nodeGroupPep.PeptideGroup,
nodePep.Peptide, nodeGroup.TransitionGroup);
var graphPointData = new GraphPointData(nodePep, nodeGroup, path);
if (addBlankPoint || paneKey.IncludesTransitionGroup(nodeGroup))
{
listPoints.Add(graphPointData);
}
if (addBlankPoint)
{
break;
}
}
}
}
// Sort into correct order
var peptideOrder = PeptideOrder;
if (peptideOrder == SummaryPeptideOrder.time)
{
if (displayTotals)
listPoints.Sort(ComparePeptideTimes);
else
listPoints.Sort(CompareGroupTimes);
}
else if (peptideOrder == SummaryPeptideOrder.area)
{
listPoints.Sort(CompareGroupAreas);
}
// Init calculated values
var pointPairLists = new List<PointPairList>();
var labels = new List<string>();
var xscalePaths = new List<IdentityPath>();
double maxY = 0;
double minY = double.MaxValue;
int selectedIndex = -1;
for (int i = 0; i < pointListCount; i++)
pointPairLists.Add(new PointPairList());
// Calculate lists and values
PeptideDocNode nodePepCurrent = null;
int chargeCount = 0, chargeCurrent = 0;
foreach (var dataPoint in listPoints)
{
var nodePep = dataPoint.NodePep;
var nodeGroup = dataPoint.NodeGroup;
if (!ReferenceEquals(nodePep, nodePepCurrent))
{
nodePepCurrent = nodePep;
chargeCount = GetChargeCount(nodePep);
chargeCurrent = 0;
}
bool addLabel = !displayTotals;
if (displayTotals && nodeGroup.TransitionGroup.PrecursorCharge != chargeCurrent)
{
LevelPointPairLists(pointPairLists);
addLabel = true;
}
chargeCurrent = nodeGroup.TransitionGroup.PrecursorCharge;
var transitionGroup = nodeGroup.TransitionGroup;
int iGroup = labels.Count;
if (addLabel)
{
string label = uniquePrefixGenerator.GetUniquePrefix(nodePep.RawTextId, nodePep.IsProteomic) +
(chargeCount > 1
? Transition.GetChargeIndicator(transitionGroup.PrecursorCharge)
: string.Empty);
if (!displayTotals && null == paneKey.IsotopeLabelType)
label += transitionGroup.LabelTypeText;
if (peptideOrder == SummaryPeptideOrder.time)
{
label += string.Format(" ({0:F01})", displayTotals ? // Not L10N
dataPoint.TimePepCharge : dataPoint.TimeGroup);
}
labels.Add(label);
xscalePaths.Add(dataPoint.IdentityPath);
}
double groupMaxY = 0;
double groupMinY = double.MaxValue;
// ReSharper disable DoNotCallOverridableMethodsInConstructor
int? resultIndex = iResult.HasValue && iResult >= 0 ? iResult : null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.best && nodePep != null)
{
resultIndex = null;
int iBest = nodePep.BestResult;
if (iBest !=-1)
resultIndex = iBest;
}
if (displayTotals)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (dictTypeToSet.ContainsKey(labelType))
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
pointPairLists[dictTypeToSet[labelType]].Add(CreatePointPair(iGroup, nodeGroup,
ref groupMaxY, ref groupMinY,
resultIndex));
}
else
{
pointPairLists[dictTypeToSet[labelType]].Add(PointPairMissing(iGroup));
}
}
}
else
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
var nodeTrans = GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
for (int i = 0; i < pointListCount; i++)
{
var pointPairList = pointPairLists[i];
pointPairList.Add(i >= nodeTrans.Length
? CreatePointPairMissing(iGroup)
: CreatePointPair(iGroup, nodeTrans[i], ref groupMaxY,
ref groupMinY,
resultIndex));
}
}
else
{
for (int i = 0; i < pointListCount; i++)
{
pointPairLists[i].Add(CreatePointPairMissing(iGroup));
}
}
}
// ReSharper restore DoNotCallOverridableMethodsInConstructor
// Save the selected index and its y extent
if (ReferenceEquals(selectedGroup, nodeGroup))
{
selectedIndex = labels.Count - 1;
SelectedMaxY = groupMaxY;
SelectedMinY = groupMinY;
}
// If multiple groups in the selection, make sure y extent is max of them
else if (selectedIndex == labels.Count - 1)
{
SelectedMaxY = Math.Max(groupMaxY, SelectedMaxY);
SelectedMinY = Math.Min(groupMinY, SelectedMinY);
}
maxY = Math.Max(maxY, groupMaxY);
minY = Math.Min(minY, groupMinY);
}
PointPairLists = pointPairLists;
Labels = labels.ToArray();
XScalePaths = xscalePaths.ToArray();
SelectedIndex = selectedIndex;
MaxY = maxY;
if (minY != double.MaxValue)
MinY = minY;
}
public override void UpdateGraph(bool selectionChanged)
{
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_No_results_available;
EmptyGraph(document);
return;
}
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode ??
GraphSummary.StateProvider.SelectedNodes.OfType <SrmTreeNode>().FirstOrDefault();
if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null)
{
EmptyGraph(document);
return;
}
Title.Text = null;
DisplayTypeChrom displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
DocNode selectedNode = selectedTreeNode.Model;
IdentityPath selectedPath = selectedTreeNode.Path;
DocNode parentNode = selectedNode;
IdentityPath parentPath = selectedTreeNode.Path;
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType != DisplayTypeChrom.single)
{
SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent;
parentNode = parentTreeNode.Model;
selectedPath = parentTreeNode.Path;
}
}
// If the selected node is a peptide with one child, then show the children,
// unless chromatogram display type is total
else if (selectedTreeNode is PeptideTreeNode)
{
var children = ((DocNodeParent)selectedNode).Children;
if (children.Count == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
selectedPath = new IdentityPath(parentPath, children[0].Id);
}
}
else if (!(selectedTreeNode is PeptideGroupTreeNode) && !(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_retention_time_graph;
CanShowRTLegend = false;
return;
}
// If a precursor is going to be displayed with display type single
if (parentNode is TransitionGroupDocNode && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!results.Chromatograms.Contains(chrom => chrom.OptimizationFunction != null))
{
displayType = DisplayTypeChrom.all;
}
}
var rtTransformOp = GraphSummary.StateProvider.GetRetentionTimeTransformOperation();
var rtValue = RTPeptideGraphPane.RTValue;
GraphValues.ReplicateGroupOp replicateGroupOp;
if (rtValue == RTPeptideValue.All)
{
replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings, GraphValues.AggregateOp.MEAN);
}
else
{
replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
}
var retentionTimeValue = new GraphValues.RetentionTimeTransform(rtValue, rtTransformOp, replicateGroupOp.AggregateOp);
YAxis.Title.Text = retentionTimeValue.GetAxisTitle();
var peptidePaths = GetSelectedPeptides().GetUniquePeptidePaths().ToList();
// if PeptideGroupTreeNode is selected but has only one child isMultiSelect should still be true
IsMultiSelect = peptidePaths.Count > 1 ||
(peptidePaths.Count == 1 &&
GraphSummary.StateProvider.SelectedNodes.FirstOrDefault() is PeptideGroupTreeNode);
GraphData graphData = new RTGraphData(document,
IsMultiSelect
? peptidePaths
: new[] { selectedPath }.AsEnumerable(), displayType, retentionTimeValue, replicateGroupOp);
CanShowRTLegend = graphData.DocNodes.Count != 0;
InitFromData(graphData);
int selectedReplicateIndex = SelectedIndex;
double minRetentionTime = double.MaxValue;
double maxRetentionTime = -double.MaxValue;
int iColor = 0, iCharge = -1;
var charge = Adduct.EMPTY;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
int colorOffset = 0;
var transitionGroupDocNode = parentNode as TransitionGroupDocNode;
if (transitionGroupDocNode != null && displayType == DisplayTypeChrom.products)
{
// If we are only displaying product ions, we want to use an offset in the colors array
// so that we do not re-use colors that would be used for any precursor ions.
colorOffset =
GraphChromatogram.GetDisplayTransitions(transitionGroupDocNode, DisplayTypeChrom.precursors).Count();
}
for (int i = 0; i < graphData.DocNodes.Count; i++)
{
var docNode = graphData.DocNodes[i];
var identityPath = graphData.DocNodePaths[i];
var pointPairLists = graphData.PointPairLists[i];
int numSteps = pointPairLists.Count / 2;
for (int iStep = 0; iStep < pointPairLists.Count; iStep++)
{
int step = iStep - numSteps;
var pointPairList = pointPairLists[iStep];
Color color;
var isSelected = false;
var nodeGroup = docNode as TransitionGroupDocNode;
if (IsMultiSelect)
{
var peptides = peptidePaths.Select(path => document.FindNode(path))
.Cast <PeptideDocNode>().ToArray();
var peptideDocNode = peptides.FirstOrDefault(
peptide => 0 <= peptide.FindNodeIndex(docNode.Id));
if (peptideDocNode == null)
{
continue;
}
color = GraphSummary.StateProvider.GetPeptideGraphInfo(peptideDocNode).Color;
if (identityPath.Equals(selectedTreeNode.Path) && step == 0)
{
color = ChromGraphItem.ColorSelected;
isSelected = true;
}
}
else if (parentNode is PeptideDocNode)
{
// Resharper code inspection v9.0 on TC gets this one wrong
// ReSharper disable ExpressionIsAlwaysNull
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
// ReSharper restore ExpressionIsAlwaysNull
color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Count];
}
else if (displayType == DisplayTypeChrom.total)
{
color = COLORS_GROUPS[iColor % COLORS_GROUPS.Count];
}
else if (ReferenceEquals(docNode, selectedNode) && step == 0)
{
color = ChromGraphItem.ColorSelected;
isSelected = true;
}
else
{
color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Count];
}
iColor++;
string label = graphData.DocNodeLabels[i];
if (step != 0)
{
label = string.Format(Resources.RTReplicateGraphPane_UpdateGraph_Step__0__, step);
}
CurveItem curveItem;
if (IsMultiSelect)
{
if (rtValue != RTPeptideValue.All)
{
curveItem = CreateLineItem(label, pointPairList, color);
}
else
{
curveItem = CreateMultiSelectBarItem(label, pointPairList, color);
}
}
else if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList))
{
curveItem = new HiLowMiddleErrorBarItem(label, pointPairList, color, Color.Black);
BarSettings.Type = BarType.Cluster;
}
else if (rtValue == RTPeptideValue.All)
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
BarSettings.Type = BarType.Cluster;
}
else
{
curveItem = CreateLineItem(label, pointPairList, color);
}
if (curveItem != null)
{
curveItem.Tag = identityPath;
var barItem = curveItem as BarItem;
if (barItem != null)
{
barItem.Bar.Border.IsVisible = false;
barItem.Bar.Fill.Brush = GetBrushForNode(docNode, color);
if (!isSelected)
{
barItem.SortedOverlayPriority = 1;
}
}
CurveList.Add(curveItem);
if (selectedReplicateIndex != -1 && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
minRetentionTime = Math.Min(minRetentionTime, pointPair.Z);
maxRetentionTime = Math.Max(maxRetentionTime, pointPair.Y);
}
}
}
}
}
// Draw a box around the currently selected replicate
if (ShowSelection && minRetentionTime != double.MaxValue)
{
AddSelection(selectedReplicateIndex, maxRetentionTime, minRetentionTime);
}
// Reset the scale when the parent node changes
if (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id))
{
XAxis.Scale.MaxAuto = XAxis.Scale.MinAuto = true;
YAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = true;
}
_parentNode = parentNode;
Legend.IsVisible = !IsMultiSelect && Settings.Default.ShowRetentionTimesLegend;
GraphSummary.GraphControl.Invalidate();
AxisChange();
}
public RTGraphData(SrmDocument document, IEnumerable <IdentityPath> selectedDocNodePaths, DisplayTypeChrom displayType, GraphValues.RetentionTimeTransform retentionTimeTransform, GraphValues.ReplicateGroupOp replicateGroupOp)
: base(document, selectedDocNodePaths, displayType, replicateGroupOp, PaneKey.DEFAULT)
{
RetentionTimeTransform = retentionTimeTransform;
}
public RTGraphData(SrmDocument document, DocNode docNode, DisplayTypeChrom displayType, GraphValues.RetentionTimeTransform retentionTimeTransform, GraphValues.ReplicateGroupOp replicateGroupOp)
: base(document, docNode, displayType, replicateGroupOp, PaneKey.DEFAULT)
{
RetentionTimeTransform = retentionTimeTransform;
}
public override void UpdateGraph(bool checkData)
{
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_No_results_available;
EmptyGraph(document);
return;
}
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode;
if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null)
{
EmptyGraph(document);
return;
}
Title.Text = null;
DisplayTypeChrom displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
DocNode selectedNode = selectedTreeNode.Model;
DocNode parentNode = selectedNode;
IdentityPath identityPath = selectedTreeNode.Path;
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType != DisplayTypeChrom.single)
{
SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent;
parentNode = parentTreeNode.Model;
identityPath = parentTreeNode.Path;
}
}
// If the selected node is a peptide with one child, then show the children,
// unless chromatogram display type is total
else if (selectedTreeNode is PeptideTreeNode)
{
var children = ((DocNodeParent)selectedNode).Children;
if (children.Count == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.RTReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_retention_time_graph;
CanShowRTLegend = false;
return;
}
// If a precursor is going to be displayed with display type single
if (parentNode is TransitionGroupDocNode && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!results.Chromatograms.Contains(chrom => chrom.OptimizationFunction != null))
{
displayType = DisplayTypeChrom.all;
}
}
var rtTransformOp = GraphSummary.StateProvider.GetRetentionTimeTransformOperation();
var rtValue = RTPeptideGraphPane.RTValue;
GraphValues.ReplicateGroupOp replicateGroupOp;
if (rtValue == RTPeptideValue.All)
{
replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings, GraphValues.AggregateOp.MEAN);
}
else
{
replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
}
var retentionTimeValue = new GraphValues.RetentionTimeTransform(rtValue, rtTransformOp, replicateGroupOp.AggregateOp);
YAxis.Title.Text = retentionTimeValue.GetAxisTitle();
GraphData graphData = new RTGraphData(document, parentNode, displayType, retentionTimeValue, replicateGroupOp);
CanShowRTLegend = graphData.DocNodes.Count != 0;
InitFromData(graphData);
int selectedReplicateIndex = SelectedIndex;
double minRetentionTime = double.MaxValue;
double maxRetentionTime = -double.MaxValue;
int iColor = 0, iCharge = -1;
int? charge = null;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
int colorOffset = 0;
var transitionGroupDocNode = parentNode as TransitionGroupDocNode;
if (transitionGroupDocNode != null && displayType == DisplayTypeChrom.products)
{
// If we are only displaying product ions, we want to use an offset in the colors array
// so that we do not re-use colors that would be used for any precursor ions.
colorOffset =
GraphChromatogram.GetDisplayTransitions(transitionGroupDocNode, DisplayTypeChrom.precursors).Count();
}
for (int i = 0; i < graphData.DocNodes.Count; i++)
{
var docNode = graphData.DocNodes[i];
var pointPairLists = graphData.PointPairLists[i];
int numSteps = pointPairLists.Count / 2;
for (int iStep = 0; iStep < pointPairLists.Count; iStep++)
{
int step = iStep - numSteps;
var pointPairList = pointPairLists[iStep];
Color color;
var nodeGroup = docNode as TransitionGroupDocNode;
if (parentNode is PeptideDocNode)
{
// Resharper code inspection v9.0 on TC gets this one wrong
// ReSharper disable ExpressionIsAlwaysNull
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
// ReSharper restore ExpressionIsAlwaysNull
color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Length];
}
else if (displayType == DisplayTypeChrom.total)
{
color = COLORS_GROUPS[iColor % COLORS_GROUPS.Length];
}
else if (docNode.Equals(selectedNode) && step == 0)
{
color = ChromGraphItem.ColorSelected;
}
else
{
color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Length];
}
iColor++;
string label = graphData.DocNodeLabels[i];
if (step != 0)
{
label = string.Format(Resources.RTReplicateGraphPane_UpdateGraph_Step__0__, step);
}
BarItem curveItem;
if (HiLowMiddleErrorBarItem.IsHiLoMiddleErrorList(pointPairList))
{
curveItem = new HiLowMiddleErrorBarItem(label, pointPairList, color, Color.Black);
}
else
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
}
if (selectedReplicateIndex != -1 && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
minRetentionTime = Math.Min(minRetentionTime, pointPair.Z);
maxRetentionTime = Math.Max(maxRetentionTime, pointPair.Y);
}
}
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
curveItem.Tag = new IdentityPath(identityPath, docNode.Id);
CurveList.Add(curveItem);
}
}
// Draw a box around the currently selected replicate
if (ShowSelection && minRetentionTime != double.MaxValue)
{
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, maxRetentionTime, 1,
maxRetentionTime - minRetentionTime, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
// Reset the scale when the parent node changes
if (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id))
{
XAxis.Scale.MaxAuto = XAxis.Scale.MinAuto = true;
YAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = true;
}
_parentNode = parentNode;
Legend.IsVisible = Settings.Default.ShowRetentionTimesLegend;
AxisChange();
}
private static bool DisplayTypeMatches(LibraryChromGroup.ChromData chromData, DisplayTypeChrom displayType)
{
switch (displayType)
{
case DisplayTypeChrom.products:
return(chromData.IonType != IonType.precursor);
case DisplayTypeChrom.precursors:
return(chromData.IonType == IonType.precursor);
default:
return(true);
}
}
// ReSharper disable PossibleMultipleEnumeration
protected GraphData(SrmDocument document, TransitionGroupDocNode selectedGroup, PeptideGroupDocNode selectedProtein,
int?iResult, DisplayTypeChrom displayType, GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp,
PaneKey paneKey)
{
RetentionTimeTransformOp = retentionTimeTransformOp;
// Determine the shortest possible unique ID for each peptide or molecule
var sequences = new List <Tuple <string, bool> >();
foreach (var nodePep in document.Molecules)
{
sequences.Add(new Tuple <string, bool>(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic));
}
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
int pointListCount = 0;
var dictTypeToSet = new Dictionary <IsotopeLabelType, int>();
bool onePointPerPeptide = PeptideOrder == SummaryPeptideOrder.document &&
null != paneKey.IsotopeLabelType;
// Figure out how many point lists to create
bool displayTotals = (displayType == DisplayTypeChrom.total);
if (displayTotals)
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
IsotopeLabelType labelType = nodeGroup.TransitionGroup.LabelType;
if (!dictTypeToSet.ContainsKey(labelType))
{
dictTypeToSet.Add(labelType, pointListCount++);
}
}
}
else
{
foreach (var nodeGroup in document.MoleculeTransitionGroups)
{
if (!paneKey.IncludesTransitionGroup(nodeGroup))
{
continue;
}
pointListCount = Math.Max(pointListCount, GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).Count());
}
}
// Build the list of points to show.
var listPoints = new List <GraphPointData>();
foreach (PeptideGroupDocNode nodeGroupPep in document.MoleculeGroups)
{
if (AreaGraphController.AreaScope == AreaScope.protein)
{
if (!ReferenceEquals(nodeGroupPep, selectedProtein))
{
continue;
}
}
foreach (PeptideDocNode nodePep in nodeGroupPep.Children)
{
bool addBlankPoint = onePointPerPeptide &&
!nodePep.TransitionGroups.Any(paneKey.IncludesTransitionGroup);
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
var path = new IdentityPath(nodeGroupPep.PeptideGroup,
nodePep.Peptide, nodeGroup.TransitionGroup);
var graphPointData = new GraphPointData(nodePep, nodeGroup, path);
if (addBlankPoint || paneKey.IncludesTransitionGroup(nodeGroup))
{
listPoints.Add(graphPointData);
}
if (addBlankPoint)
{
break;
}
}
}
}
// Sort into correct order
var peptideOrder = PeptideOrder;
if (peptideOrder == SummaryPeptideOrder.time)
{
if (displayTotals)
{
listPoints.Sort(ComparePeptideTimes);
}
else
{
listPoints.Sort(CompareGroupTimes);
}
}
else if (peptideOrder == SummaryPeptideOrder.area)
{
listPoints.Sort(CompareGroupAreas);
}
else if (peptideOrder == SummaryPeptideOrder.mass_error)
{
listPoints.Sort(CompareGroupMassErrors);
}
// Init calculated values
var pointPairLists = new List <PointPairList>();
var labels = new List <string>();
var xscalePaths = new List <IdentityPath>();
double maxY = 0;
double minY = double.MaxValue;
int selectedIndex = -1;
for (int i = 0; i < pointListCount; i++)
{
pointPairLists.Add(new PointPairList());
}
// Calculate lists and values
PeptideDocNode nodePepCurrent = null;
int chargeCount = 0;
var chargeCurrent = Adduct.EMPTY;
foreach (var dataPoint in listPoints)
{
var nodePep = dataPoint.NodePep;
var nodeGroup = dataPoint.NodeGroup;
if (!ReferenceEquals(nodePep, nodePepCurrent))
{
nodePepCurrent = nodePep;
chargeCount = GetChargeCount(nodePep);
chargeCurrent = Adduct.EMPTY;
}
bool addLabel = !displayTotals;
if (displayTotals && !Equals(nodeGroup.TransitionGroup.PrecursorAdduct, chargeCurrent))
{
LevelPointPairLists(pointPairLists);
addLabel = true;
}
chargeCurrent = nodeGroup.TransitionGroup.PrecursorAdduct;
var transitionGroup = nodeGroup.TransitionGroup;
int iGroup = labels.Count;
if (addLabel)
{
string label = uniquePrefixGenerator.GetUniquePrefix(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic) +
(chargeCount > 1
? Transition.GetChargeIndicator(transitionGroup.PrecursorAdduct)
: string.Empty);
if (!displayTotals && null == paneKey.IsotopeLabelType)
{
label += transitionGroup.LabelTypeText;
}
if (peptideOrder == SummaryPeptideOrder.time)
{
label += string.Format(@" ({0:F01})", displayTotals ?
dataPoint.TimePepCharge : dataPoint.TimeGroup);
}
labels.Add(label);
xscalePaths.Add(dataPoint.IdentityPath);
}
double groupMaxY = 0;
double groupMinY = double.MaxValue;
// ReSharper disable DoNotCallOverridableMethodsInConstructor
int?resultIndex = iResult.HasValue && iResult >= 0 ? iResult : null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.best && nodePep != null)
{
resultIndex = null;
int iBest = nodePep.BestResult;
if (iBest != -1)
{
resultIndex = iBest;
}
}
if (displayTotals)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (dictTypeToSet.ContainsKey(labelType))
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
pointPairLists[dictTypeToSet[labelType]].Add(CreatePointPair(iGroup, nodeGroup,
ref groupMaxY, ref groupMinY,
resultIndex));
}
else
{
pointPairLists[dictTypeToSet[labelType]].Add(PointPairMissing(iGroup));
}
}
}
else
{
if (paneKey.IncludesTransitionGroup(nodeGroup))
{
var nodeTrans = GraphChromatogram.GetDisplayTransitions(nodeGroup, displayType).ToArray();
for (int i = 0; i < pointListCount; i++)
{
var pointPairList = pointPairLists[i];
pointPairList.Add(i >= nodeTrans.Length
? CreatePointPairMissing(iGroup)
: CreatePointPair(iGroup, nodeTrans[i], ref groupMaxY,
ref groupMinY,
resultIndex));
}
}
else
{
for (int i = 0; i < pointListCount; i++)
{
pointPairLists[i].Add(CreatePointPairMissing(iGroup));
}
}
}
// ReSharper restore DoNotCallOverridableMethodsInConstructor
// Save the selected index and its y extent
if (ReferenceEquals(selectedGroup, nodeGroup))
{
selectedIndex = labels.Count - 1;
SelectedMaxY = groupMaxY;
SelectedMinY = groupMinY;
}
// If multiple groups in the selection, make sure y extent is max of them
else if (selectedIndex == labels.Count - 1)
{
SelectedMaxY = Math.Max(groupMaxY, SelectedMaxY);
SelectedMinY = Math.Min(groupMinY, SelectedMinY);
}
maxY = Math.Max(maxY, groupMaxY);
minY = Math.Min(minY, groupMinY);
}
PointPairLists = pointPairLists;
Labels = labels.ToArray();
XScalePaths = xscalePaths.ToArray();
SelectedIndex = selectedIndex;
MaxY = maxY;
if (minY != double.MaxValue)
{
MinY = minY;
}
}
private void DisplayTransitions(IRegressionFunction timeRegressionFunction,
TransitionDocNode nodeTranSelected,
ChromatogramSet chromatograms,
float mzMatchTolerance,
TransitionGroupDocNode nodeGroup,
ChromatogramGroupInfo chromGroupInfo,
PaneKey graphPaneKey,
DisplayTypeChrom displayType,
ref double bestStartTime,
ref double bestEndTime)
{
var fileId = chromatograms.FindFile(chromGroupInfo);
// Get points for all transitions, and pick maximum peaks.
ChromatogramInfo[] arrayChromInfo;
var displayTrans = GetDisplayTransitions(nodeGroup, displayType).ToArray();
int numTrans = displayTrans.Length;
int numSteps = 0;
bool allowEmpty = false;
if (IsSingleTransitionDisplay && nodeTranSelected != null)
{
if (!displayTrans.Contains(nodeTranSelected))
{
arrayChromInfo = new ChromatogramInfo[0];
displayTrans = new TransitionDocNode[0];
numTrans = 0;
}
else
{
arrayChromInfo = chromGroupInfo.GetAllTransitionInfo((float) nodeTranSelected.Mz,
mzMatchTolerance,
chromatograms.OptimizationFunction);
if (chromatograms.OptimizationFunction != null)
{
// Make sure the number of steps matches what will show up in the summary
// graphs, or the colors won't match up.
int numStepsExpected = chromatograms.OptimizationFunction.StepCount*2 + 1;
if (arrayChromInfo.Length != numStepsExpected)
{
arrayChromInfo = ResizeArrayChromInfo(arrayChromInfo, numStepsExpected);
allowEmpty = true;
}
}
numTrans = arrayChromInfo.Length;
displayTrans = new TransitionDocNode[numTrans];
for (int i = 0; i < numTrans; i++)
displayTrans[i] = nodeTranSelected;
}
numSteps = numTrans/2;
}
else
{
arrayChromInfo = new ChromatogramInfo[numTrans];
for (int i = 0; i < numTrans; i++)
{
var nodeTran = displayTrans[i];
// Get chromatogram info for this transition
arrayChromInfo[i] = chromGroupInfo.GetTransitionInfo((float) nodeTran.Mz, mzMatchTolerance);
}
}
int bestPeakTran = -1;
TransitionChromInfo tranPeakInfo = null;
float maxPeakHeight = float.MinValue;
int numPeaks = chromGroupInfo.NumPeaks;
var maxPeakTrans = new int[numPeaks];
var maxPeakHeights = new float[numPeaks];
for (int i = 0; i < numPeaks; i++)
maxPeakHeights[i] = float.MinValue;
var transform = Transform;
// Prepare arrays of values for library dot-product
double[] expectedIntensities = null;
double[][] peakAreas = null;
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = DocumentUI.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if ((isFullScanMs && !isShowingMsMs && nodeGroup.HasIsotopeDist) ||
(!isFullScanMs && nodeGroup.HasLibInfo))
{
expectedIntensities = new double[numTrans];
peakAreas = new double[numPeaks][];
for (int i = 0; i < numPeaks; i++)
peakAreas[i] = new double[numTrans];
}
// Find the transition with the maximum peak height for the best peak
for (int i = 0; i < numTrans; i++)
{
var nodeTran = displayTrans[i];
int step = (numSteps > 0 ? i - numSteps : 0);
var transitionChromInfo = GetTransitionChromInfo(nodeTran, _chromIndex, fileId, step);
if (transitionChromInfo == null)
continue;
if (maxPeakHeight < transitionChromInfo.Height)
{
maxPeakHeight = transitionChromInfo.Height;
bestPeakTran = i;
tranPeakInfo = transitionChromInfo;
}
AddBestPeakTimes(transitionChromInfo, ref bestStartTime, ref bestEndTime);
}
for (int i = 0; i < numTrans; i++)
{
var nodeTran = displayTrans[i];
// Store library intensities for dot-product
if (expectedIntensities != null)
{
if (isFullScanMs)
expectedIntensities[i] = nodeTran.HasDistInfo ? nodeTran.IsotopeDistInfo.Proportion : 0;
else
expectedIntensities[i] = nodeTran.HasLibInfo ? nodeTran.LibInfo.Intensity : 0;
}
var info = arrayChromInfo[i];
if (info == null)
continue;
// Apply any active transform
info.Transform(transform);
for (int j = 0; j < numPeaks; j++)
{
var peak = info.GetPeak(j);
// Exclude any peaks between the boundaries of the chosen peak.
if (IntersectPeaks(peak, tranPeakInfo))
continue;
// Store peak intensity for dot-product
if (peakAreas != null)
peakAreas[j][i] = peak.Area;
// Keep track of which transition has the max height for each peak
if (maxPeakHeights[j] < peak.Height)
{
maxPeakHeights[j] = peak.Height;
maxPeakTrans[j] = i;
}
}
}
// Calculate library dot-products, if possible
double[] dotProducts = null;
double bestProduct = 0;
int minProductTrans = isFullScanMs
? TransitionGroupDocNode.MIN_DOT_PRODUCT_MS1_TRANSITIONS
: TransitionGroupDocNode.MIN_DOT_PRODUCT_TRANSITIONS;
if (peakAreas != null && numTrans >= minProductTrans)
{
var tranGroupChromInfo = GetTransitionGroupChromInfo(nodeGroup, fileId, _chromIndex);
double? dotProduct = null;
if (tranGroupChromInfo != null)
{
dotProduct = isFullScanMs
? tranGroupChromInfo.IsotopeDotProduct
: tranGroupChromInfo.LibraryDotProduct;
}
if (dotProduct.HasValue)
{
bestProduct = dotProduct.Value;
var statExpectedIntensities = new Statistics(expectedIntensities);
for (int i = 0; i < peakAreas.Length; i++)
{
var statPeakAreas = new Statistics(peakAreas[i]);
double dotProductCurrent = statPeakAreas.NormalizedContrastAngleSqrt(statExpectedIntensities);
// Only show products that are greater than the best peak product,
// and by enough to be a significant improvement. Also the library product
// on the group node is stored as a float, which means the version
// hear calculated as a double can be larger, but really represent
// the same number.
if (dotProductCurrent > bestProduct &&
dotProductCurrent > 0.5 &&
dotProductCurrent - bestProduct > 0.05)
{
if (dotProducts == null)
dotProducts = new double[numPeaks];
dotProducts[i] = dotProductCurrent;
}
}
}
}
// Create graph items
int iColor = 0;
int lineWidth = LineWidth;
float fontSize = FontSize;
// We want the product ion colors to stay the same whether they are displayed:
// 1. In a single pane with the precursor ions (Transitions -> All)
// 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph)
// 3. In a single pane by themselves (Transition -> Products)
// We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors.
var nodeDisplayType = GetDisplayType(DocumentUI, nodeGroup);
int colorOffset = 0;
if(displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && chromatograms.OptimizationFunction == null)))
{
colorOffset = GetDisplayTransitions(nodeGroup, DisplayTypeChrom.precursors).Count();
}
for (int i = 0; i < numTrans; i++)
{
var info = arrayChromInfo[i];
if (info == null && !allowEmpty)
continue;
var nodeTran = displayTrans[i];
int step = numSteps != 0 ? i - numSteps : 0;
Color color;
bool shade = false;
int width = lineWidth;
if ((numSteps == 0 && ReferenceEquals(nodeTran, nodeTranSelected) ||
(numSteps > 0 && step == 0)))
{
color = ChromGraphItem.ColorSelected;
shade = true;
width++;
}
else
{
color = COLORS_LIBRARY[(iColor + colorOffset) % COLORS_LIBRARY.Length];
}
TransitionChromInfo tranPeakInfoGraph = null;
if (bestPeakTran == i)
tranPeakInfoGraph = tranPeakInfo;
var scanName = nodeTran.FragmentIonName;
if (nodeTran.Transition.Charge != 1) // Positive singly charged is uninteresting
scanName += Transition.GetChargeIndicator(nodeTran.Transition.Charge);
if (nodeTran.Transition.MassIndex != 0)
scanName += Environment.NewLine + Transition.GetMassIndexText(nodeTran.Transition.MassIndex);
var fullScanInfo = new FullScanInfo
{
ChromInfo = info,
ScanName = scanName
};
if (fullScanInfo.ChromInfo != null && fullScanInfo.ChromInfo.ExtractionWidth > 0)
_enableTrackingDot = true;
var graphItem = new ChromGraphItem(nodeGroup,
nodeTran,
info,
tranPeakInfoGraph,
timeRegressionFunction,
GetAnnotationFlags(i, maxPeakTrans, maxPeakHeights),
dotProducts,
bestProduct,
isFullScanMs,
false,
step,
color,
fontSize,
width,
fullScanInfo);
_graphHelper.AddChromatogram(graphPaneKey, graphItem);
if (shade)
{
ShadeGraph(tranPeakInfo,info,timeRegressionFunction,dotProducts,bestProduct,isFullScanMs,step,fontSize,width,fullScanInfo,graphPaneKey);
}
iColor++;
}
var graphPane = _graphHelper.GetGraphPane(graphPaneKey);
if (graphPane == null)
_enableTrackingDot = false;
if (_enableTrackingDot)
{
graphPane.CurveList.Insert(FULLSCAN_TRACKING_INDEX, CreateScanPoint(Color.Black));
graphPane.CurveList.Insert(FULLSCAN_SELECTED_INDEX, CreateScanPoint(Color.Red));
}
}
protected override GraphData CreateGraphData(SrmDocument document, PeptideGroupDocNode selectedProtein, TransitionGroupDocNode selectedGroup, DisplayTypeChrom displayType)
{
int?result = null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.single)
{
result = GraphSummary.ResultsIndex;
}
return(new AreaGraphData(document, selectedGroup, selectedProtein, result, displayType, PaneKey));
}
public static IEnumerable<TransitionDocNode> GetDisplayTransitions(TransitionGroupDocNode nodeGroup,
DisplayTypeChrom displayType)
{
switch (displayType)
{
case DisplayTypeChrom.precursors:
// Return transitions that would be filtered from MS1
return nodeGroup.GetMsTransitions(true);
case DisplayTypeChrom.products:
// Return transitions that would not be filtered in MS1
return nodeGroup.GetMsMsTransitions(true);
default:
return nodeGroup.Transitions;
}
}
public void SetDisplayTypeChrom(DisplayTypeChrom displayType)
{
Settings.Default.ShowTransitionGraphs = displayType.ToString();
UpdateChromGraphs();
UpdateSpectrumGraph(false);
UpdateRetentionTimeGraph();
UpdatePeakAreaGraph();
}
protected abstract GraphData CreateGraphData(SrmDocument document, PeptideGroupDocNode selectedProtein,
TransitionGroupDocNode selectedGroup, DisplayTypeChrom displayType);
protected GraphData(SrmDocument document, IdentityPath identityPath, DisplayTypeChrom displayType, ReplicateGroupOp replicateGroupOp, PaneKey paneKey)
: this(document, new[] { identityPath }, displayType, replicateGroupOp, paneKey)
{
}
protected override GraphData CreateGraphData(SrmDocument document, PeptideGroupDocNode selectedProtein, TransitionGroupDocNode selectedGroup, DisplayTypeChrom displayType)
{
int?result = null;
if (RTLinearRegressionGraphPane.ShowReplicate == ReplicateDisplay.single)
{
result = GraphSummary.ResultsIndex;
}
return(new RTGraphData(document, selectedGroup, selectedProtein, result, displayType, GraphSummary.StateProvider.GetRetentionTimeTransformOperation()));
}
private List <PointPairList> MakePointPairLists <TChromInfoData>(
DisplayTypeChrom displayType,
IList <ICollection <TChromInfoData> > chromInfoResults,
Func <TChromInfoData, bool> isMissingValue,
Func <int, ICollection <TChromInfoData>, PointPair> createPointPair) where TChromInfoData : ChromInfoData
{
var pointPairLists = new List <PointPairList>();
if (null == chromInfoResults)
{
pointPairLists.Add(new PointPairList());
return(pointPairLists);
}
int maxSteps = 1;
bool allowSteps = (displayType == DisplayTypeChrom.single);
if (allowSteps)
{
foreach (var result in chromInfoResults)
{
maxSteps = Math.Max(maxSteps, GetCountSteps(result));
}
}
for (int i = 0; i < maxSteps; i++)
{
pointPairLists.Add(new PointPairList());
}
int numSteps = maxSteps / 2;
IList <ReplicateGroup> replicateGroups = _replicateGroups;
for (int iGroup = 0; iGroup < replicateGroups.Count; iGroup++)
{
// Fill everything with missing data until filled for real
foreach (PointPairList pairList in pointPairLists)
{
pairList.Add(PointPairMissing(iGroup));
}
var replicateGroup = replicateGroups[iGroup];
var chromInfoLists = new List <ICollection <TChromInfoData> >();
foreach (var replicateIndex in replicateGroup.ReplicateIndexes)
{
if (replicateIndex < 0 || replicateIndex >= chromInfoResults.Count)
{
continue;
}
chromInfoLists.Add(chromInfoResults[replicateIndex]);
}
if (0 == chromInfoLists.Count)
{
continue;
}
var optimizationSteps = chromInfoLists
.SelectMany(chromInfoList => from chromInfoData in chromInfoList
where chromInfoData.ChromInfo != null
select chromInfoData.OptimizationStep)
.Distinct()
.ToArray();
foreach (int step in optimizationSteps)
{
int iStep = step + numSteps;
if (0 > iStep || iStep >= pointPairLists.Count)
{
continue;
}
var chromInfoDatasForStep = new List <TChromInfoData>();
foreach (var chromInfoDatas in chromInfoLists)
{
var chromInfosForStep = new List <TChromInfoData>();
if (replicateGroup.FileInfo != null)
{
var info = chromInfoDatas.FirstOrDefault(chromInfoData => chromInfoData != null && chromInfoData.ChromFileInfo.Equals(replicateGroup.FileInfo) && step == chromInfoData.OptimizationStep);
chromInfosForStep.Add(info);
}
else
{
var step1 = step;
var chromInfos =
chromInfoDatas.Where(
chromInfoData => chromInfoData != null &&
step1 == chromInfoData.OptimizationStep);
chromInfosForStep.AddRange(chromInfos);
}
chromInfoDatasForStep.AddRange(chromInfosForStep.Where(c => c != null && !isMissingValue(c)));
}
var pointPairList = pointPairLists[iStep];
pointPairList[pointPairList.Count - 1] = createPointPair(iGroup, chromInfoDatasForStep);
}
}
return(pointPairLists);
}
public RTGraphData(SrmDocument document,
TransitionGroupDocNode selectedGroup,
PeptideGroupDocNode selectedProtein,
int? result,
DisplayTypeChrom displayType,
GraphValues.IRetentionTimeTransformOp retentionTimeTransformOp
)
: base(document, selectedGroup, selectedProtein, result, displayType, retentionTimeTransformOp, PaneKey.DEFAULT)
{
}
